This paper is concerned with flight controller design of D-SEND#2. D-SEND is a project to demonstrate a low sonic boom aerodynamic design concept. In the #2 part of this project, an unpowered test vehicle is lifted to an altitude of 30km by a balloon from which it then separates. After the separation, the vehicle's on-board flight control computer selects a target Boom Measurement System (BMS) according to the separation point. The vehicle then autonomously flies to the selected BMS and establishes prescribed sonic boom measurement flight conditions. The design of the GNC system for D-SEND#2 project is exceptionally challenging since 1) there is no nominal trajectory, 2) there is only limited control available to meet various requirements, 3) the flight envelope is quite wide, and 4) the development time is short. Dynamic inversion method and time-scale separation technique are applied to deal with these problems, and a systematic controller design procedure is presented. The controller is designed with this procedure and evaluated through linear analysis and Monte-Carlo simulations which shows it has sufficient performance and safety margines. This controller design method is confirmed to be a practical method for UAVs.